The long-term course of migraine with aura (MA) has been poorly explored. The present 11-year follow-up study assessed the long-term natural history and possible prognostic factors of MA with onset in childhood or adolescence. Patients were recruited from the original case records of our department, which are specifically designed to report all headache characteristics, aura symptoms and electroencephalogram (EEG) findings. A total of 77 patients (47 females; 30 males) whose records contained detailed descriptions of both headache and aura symptoms apparently meeting the International Classification of Headache Disorders (ICHD)-II criteria for MA (i.e., 1.2.1, 1.2.2, 1.2.6) underwent structured face-to-face follow-up headache interviews, all of which were conducted by the same neurologist, who has particular expertise in this field. A multivariate model (logistic regression analysis) was used to investigate the association between possible prognostic factors and the remission of both aura and headache at follow-up. The results of our study showed that 23.4% of the MA patients were headache-free at follow-up, 44.1% still had MA and 32.5% had a transformed headache diagnosis (i.e., fulfilling the criteria for ICHD-II 1.1. or 2). Patients with basilar-type migraine (1.2.6) showed the highest headache remission rate (38.5%). Our study seems to show that migraine with typical aura (1.2.1–1.2.2) is associated with a favourable evolution of aura symptoms over time (remission of aura in 54.1% of patients). Subjects experiencing only visual aura had a lower remission rate compared with those with visual ± sensory ± aphasic aura symptoms (36.8% vs. 61.5%, p = 0.054). A short headache duration (<12 hrs) and the presence of EEG abnormalities at baseline were the only significant predictors of aura remission at follow-up (odds ratio [OR] = 9.12, 95% confidence interval [CI]: 1.79 ± 46.51, and OR = 4.76, 95% CI: 1.18 ± 19.15, respectively). No significant predictors of headache remission were found. In conclusion, our results suggest that MA shows a favourable course. Further prospective studies with detailed EEG analysis both at baseline and at follow-up are needed in order to confirm the possible prognostic role of EEG abnormalities in MA. That said, it would, in our opinion, be highly premature at present to submit children with MA to EEG examinations for prognostication purposes.